sswu_script

Utility scripts for microbial data processing.

OTU Statistics

The python/otu_stat.py script filters bacteria based on abundance across sample groups.

Requirements

• Python 3.8+
• pandas

Usage

python python/otu_stat.py <abundance_matrix.csv> <grouping.csv> \
    -o results.txt -t 0.1 -p 0.8

Arguments

• abundance_matrix: CSV file where rows are bacteria and columns are samples.
• grouping: CSV file with two columns: sample name and group.
• -o, --output: Path for the output file (default otu_stat_results.txt).
• -t, --threshold: Abundance threshold to consider a bacterium present (default 0.1).
• -p, --proportion: Minimum fraction of samples in a group that must meet the threshold (default 0.8).

The output lists, for each group, bacteria whose abundance exceeds the threshold in at least the specified proportion of samples.